this is super useful!

New preprint. I've been chewing on why bacteria have pangenomes for years. Most species carry a distributed gene pool far larger than any one genome holds. E. coli has ~163,000 rare genes across the species. Each individual cell carries about 5,000. Why? A 🧵👇

New results from our synthetic communities, antibiotics & resilience project: Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation www.biorxiv.org/content/10.6... Work led by @jcairns.bsky.social

Can we reconstruct ancient pathogen genomes from animal remains? Can paleopathology help prioritize promising specimens? Our new paper demonstrates this by screening more than 300 specimens from across Eurasia over the past 6,000 years. www.nature.com/articles/s41...

🚨FULLY FUNDED PHD POSITION!🚨 If you are interested in trying to answer the question of "How did climate shape the movements, interactions, and evolution of hominin populations?" Come join my lab at @humanorigins.bsky.social 🧬🧪 deadline 7th of June ⬇️ uni-tuebingen.de/universitaet...

Really excited to share a fully-funded PhD position in my lab at the University of Reading exploring how E. coli uses competition to survive in the microbiome. Perfect for anyone interested in using a mix of biochem and ecology to study pathogens. Deadline May 29th! www.findaphd.com/phds/project...

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

My main postdoc paper is now out in @natureportfolio.nature.com npj Antimicrobials and Resistance! www.nature.com/articles/s44.... Using flow cytometry, we show that the nucleoside analogues azidothymidine, didanosine, stavudine, and trifluridine reduced transfer of AMR plasmids pCT and pKpQIL (1/3)

LLMs are like your stoner friend who is a voracious reader. They have a lot of information in their brains, but it's not necessarily in the right order, and sometimes they talk utter nonsense.

📢 Excited to be offering a Plant Health vacation studentship this summer on plant disease biocontrol and predatory bacteria! Supervised by me at Manchester Uni! @manchester.ac.uk If interested—or know someone who might be—please share and apply! my.rsb.org.uk/services.php... 28th April deadline 🌿🍅🦠

would 100% recommend this as a PhD position to anyone interested in bacteria/temperature/amr. Dan is a great scientist to work with, and more importantly is a kind person who cares about people and (also) how science works

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

Is virulence a fixed trait? This first commentary in Microbiology Outlooks considers why it may be better understood as a context-dependent evolutionary strategy. Discover the Open Access article: https://doi.org/10.1099/mout.0.00001

🚨 New preprint 🚨 How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence? A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship! www.biorxiv.org/content/10.6...

📣 2026 PhD studentship 📣 Via @manchester.ac.uk 's President's Doctoral Scholar Awards, we are encouraging applications for a PhD on the effect of pollutant exposure on microbe-immune cross talk. This project will incorporate microbiology, immunology, & bioinformatics. Deadline: 16 March 2026!

He may have only barely known about bacteria, and not at all about viruses, but Darwin was right about hating an ill-defined species concept

The coolest finding of my PhD is finally out! E. coli has a 7th RND pump that is present in phylogroups B2/D/E/F but absent in A/B1/C. As a result EefABC has been absent in all K-12 RND studies! Co-authored by the very talented Dr. Lizzy Darby. @jessicamablair.bsky.social doi.org/10.1099/mgen...

Delighted to have contributed to this impressive work led by @tovefall.bsky.social & many others👏 (w/ @gazollavolpiano.bsky.social from our side). This novel microbiome GWAS (n=~16k+12k valid) expands knowledge on genetic factors associated w/ gut microbiota variation. www.nature.com/articles/s41...

Now out & nicely formatted in @isme-microbes.bsky.social A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron. A few highlights... 🧵 (1/n) doi.org/10.1093/isme...

I am pleased to share that our paper is now published in Cell! www.cell.com/cell/fulltex... I am deeply grateful to all co-authors for making this possible. This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.

🚨 PhD Studentship available! 🚨 We're hiring a UK student to start in Oct '26 via the BBSRC CODEM scheme. Full studentship plus £10k top-up PA. Study the mysterious ZOMBIE PHAGES 🧟 🦠 with our fabulous @mermanchester.bsky.social and @uommib.bsky.social communities! www.findaphd.com/phds/project...

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

Historical contingency limits adaptive diversification in a spatially structured environment @evolletters.bsky.social from @megbehri.bsky.social academic.oup.com/evlett/artic...

New round of PhD studentships in microbial engineering, including one with me on engineering non-canonical DNA mismatch repair into E. coli 🦠🧬 www.findaphd.com/phds/project...

PhD projects in microbial engineering now up, including one with @whelanfj.bsky.social @willpjsmith.bsky.social and me! 🦠 www.findaphd.com/phds/project...

Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...

🚨 Fully‑funded PhD for Home Students🚨 We'll explore non-antibiotic alternatives in relatistic environments, uncovering how they work, if they affect antibiotic activity and whether they influcence AMR acquistion. Come join a wonderful supervisory team! #MicroSky #UTISky #AMar tinyurl.com/38u552bu

It's easier to tear down than build up, and in science we have a bad case of that. So: how to lead a journal club that actually finds value in what you read. scientistseessquirre... 🧪

"84.9% of colleagues on FTCs reported that their contracts had negative impacts upon their wellbeing" ^ As long as fixed-term contracts (FTC's) are the norm for early-career scholars + many others, then our workplaces are structurally screwing us.

There's still a few days left to apply for our AI-Intervene PhD project mapping the drivers of avian influenza using viral genomics, bird migration data and AI-powered phylodynamics. Come join us! Details below. #FindaPhD #LondonPhD #genomics

Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.

🦠🧫 a collaboration with the Institute for Tropical Medicine in Tübingen and CERMEL in Gabon @cmfi.bsky.social

Asexuality is a global identity. That’s a major finding in a study I recently published with @francescorampazzo.com in Demographic Research. Analyzing dating app data spanning 162 countries from over 900,000 users, we found that asexuality showed up in every age group and in every region.

MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

It’s not only medications—environmental chemicals can also inadvertently harm our gut microbes. Excited to have contributed a bit to this important study!

🚨‼️ New paper alert! ‘Sewers to Seas: exploring pathogens and antimicrobial resistance on microplastics from hospital wastewater to marine environments’ FULL ARTICLE: www.sciencedirect.com/science/arti... ➡️ Check out @pml.ac.uk’s coverage: pml.ac.uk/news/micropl...

Great to see our @exeter.ac.uk and @pml.ac.uk research highlighted in @uk.theconversation.com 🤟🙏 ➡️ theconversation.com/plastic-bio-...

Are you looking for a wild PhD opportunity? 🦠🧵 There are several opportunities to join the Wild Microbiome Lab in 2026! Scroll for more information, or visit the link below for full project descriptions and application information👇 xavharrison.github.io

Exciting PhD position on algal-driven metal remediation with Dr Michiel Vos and collaborators at the University of Exeter. This project combines plant and microbial ecology, and geochemistry to develop innovative biological solutions for metal pollution www.findaphd.com/phds/project...

📢 New paper in @natcomms.nature.com Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes doi.org/10.1038/s414... Thrilled to share this massive global effort led by H.M. Martiny, @patrickmunk.bsky.social, F. Aarestrup & the Global Sewage Consortium

A lot has happened since our first announcement of #ExE2026, an evolutionary ecology conference hosted by @uniexecec.bsky.social in #Cornwall from June 29 to July 3 2026. Have a look at our new website to see our confirmed plenary speakers, the mid-conference excursions, and more. 👉 evoxeco.uk 👈

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics We just did that to study the history of #AMR spread @science.org doi.org/10.1126/scie... If you like time travel & biology, this 🧵is for you👇

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)! We're looking for someone keen on bioinformatics and microbiome evolution. Important info below on eligibility & URSA competition funding👇 www.findaphd.com/phds/project...

Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published! proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...

We have a new preprint modeling the regulatory networks of efflux pumps to predict the evolution of multidrug resistance in P. aeruginosa. Also explore cross-resistance, collateral sensitivity & loss of resistance. With @suvamroy.bsky.social @elibbyscience.bsky.social www.biorxiv.org/content/10.1...

🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️ Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...

PhD studentship opportunity! Join us at St Andrews to study the factors controlling plasmid transmission in the gut. Competition-funded as part of the EASTBIO DTP, co-supervised with Dr Jaclyn Pearson. Please share & pass on to anyone interested! 🦠🧫 Deadline 15th December👇

‘The latest surveillance data found that the number of antibiotic-resistant infections in 2024 equated to an average of nearly 400 newly reported cases a week.’ www.theguardian.com/society/2025...